Background: HIV/AIDS continues to be a major public health concern for children. Each day, worldwide, approximately 440 children became newly infected with HIV, and 270 children died from AIDS-related causes in 2018. Poor nutrition has been associated with accelerated disease progression, and sufficient dietary diversity is considered a key to improve children’s nutritional status. Therefore, this study aims to 1) examine nutritional status of school-age children living with HIV in Phnom Penh, Cambodia, and 2) identify factors associated with their nutritional status, especially taking their dietary diversity into consideration. Methods: This cross-sectional study was conducted in May 2018 within the catchment area of the National Pediatric Hospital, Cambodia. Data from 298 children and their caregivers were included in the analyses. Using semi-structured questionnaires, face-to-face interviews were conducted to collect data regarding sociodemographic characteristics, quality of life, and dietary diversity. To assess children’s nutritional status, body weight and height were measured. Viral load and duration of antiretroviral therapy (ART) were collected from clinical records. Multiple logistic regression analyses were performed to identify factors associated with stunting and wasting. Results: Of 298 children, nearly half (46.6%) were stunted, and 13.1% were wasted. The mean number of food groups consumed by the children in the past 24 hours was 4.6 out of 7 groups. Factors associated with children’s stunting were age (adjusted odds ratio [AOR] 2.166, 95% confidence interval [CI]: 1.151, 4.077), household wealth (AOR 0.543, 95%CI: 0.299, 0.986), duration of receiving ART (AOR 0.510, 95%CI: 0.267, 0.974), and having disease symptoms during the past one year (AOR 1.871, 95%CI: 1.005, 3.480). The only factor associated with wasting was being male (AOR 5.304, 95%CI: 2.210, 12.728). Conclusions: Prevalence of stunting was more than double that of non-infected school-age children living in urban areas in Cambodia. This highlights the importance of conducting nutritional intervention programs, especially tailored for children living with HIV in the country. Although dietary diversity was not significantly associated with children’s nutritional status in this study, the findings will contribute to implementing future nutritional interventions more efficiently by indicating children who are most in need of such interventions in Cambodia.